I don't think an area plot allows for multiple colors within a single area object. You could accomplish the color change using a patch object instead, but then you need to manually add the appropriate baseline:
n = 10;
Le = 10000;
xn = linspace(0,Le,n+1);
T = 89250-357*xn/20;
xp = [xn xn(end) xn(1) xn(1)];
yp = [T 0 0 T(1)];
cp = sign(yp);
hp = patch(xp, yp, cp);
set(gca, 'clim', [-1 1], 'colormap', [1 0 0; 0 0 1]);
I think it would be more straightforward to just use two area objects instead:
T1 = max(T, 0);
T2 = min(T, 0);
taglio1 = area(xn, T1, 'facecolor', 'b');
hold on;
taglio2 = area(xn, T2, 'facecolor', 'r');
